A workflow depicting the steps involved in mass spectrometry data analysis for genome annotation purposes. In this case, the tryptic peptide mixture derived from digestion of Anopheles gambiae salivary gland proteins was analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS). The mass spectrometry data was searched against the NCBI non-redundant protein database to identify known or novel transcripts from An. gambiae. The data was also searched against the An. gambiae genome database to identify novel protein-coding genes. A careful bioinformatics analysis was performed to use peptide data for correcting genomic annotations.